prepare.miniseq.specifications {varitas}

prepare.miniseq.specifications

Description

Process a MiniSeq directory and sample sheet to get specification data frames that can be used to run the VariTAS pipeline.

Note: This assumes normal samples are not available.

Usage

prepare.miniseq.specifications(sample.sheet, miniseq.directory)

Arguments

sample.sheet

Data frame containing sample information, or path to a MiniSeq sample sheet

miniseq.directory

Path to directory with MiniSeq files

Value

A list with specification data frames 'fastq', 'bam', and 'vcf' (as applicable)

Examples

miniseq.sheet <- file.path(path.package('varitas'), 'extdata/miniseq/Example_template.csv')
miniseq.directory <- file.path(path.package('varitas'), 'extdata/miniseq')
miniseq.info <- prepare.miniseq.specifications(miniseq.sheet, miniseq.directory)